Does the controller have motor protection logic/timers to detect if the motor is stalled?

This sounds like normal behavior I discovered with the TAPR TakBox. There is a timer that detects if the ADC disagrees with where the controller thinks the rotor should be pointed and stops the motor. It takes a number of seconds (in the timer) to reset the controller.

What I found was that the ADC always lagged where the controller thought the antenna should be pointed. The timer had to be long enough to allow the rotor to catch up.

"The trouble is, no matter what software I use, or even if I manually issue pointing commands via serial terminal, the ST2 will stop my rotator too early, resulting in offpointing by about 20 degrees. I am using the same voltage divider that I used on my KCT, so the ST2 is seeing a 0-5v reading from the azimuth rotor POT. The LCD display matches the analog display within a degree, so the ST2 knows correctly where the azimuth rotator is aimed."